Neither of these will matter because the Interact with Target Mapped Key in ISBoxer turns CTM on and off.Auto-activate CTM on slaves is off. CTM under interface options is also off.
Anyway, it's amazing how being able to clearly explain the problem actually helps you to work out the solution sometimes.
The difference in behaviour you have noted between the 1 key on one hand and the 2,3,4 keys on the other is that your "DPS 1" Mapped Key includes an action that performs IWT while your "DPS 2" Mapped Key does not.
What you need to do is set things up so that only Characters in your Melee Action Target Group interact with the target. If you don't put your priest in this group it will no longer IWT.
1. In the General Key Map, right click Interact with Target, choose Make Copy. Select the copy (Copy of Interact with Target), hit F2 and rename it as "Interact with Target Melee".
2. Change the Hotkey for "Interact with Target Melee" to <NO KEY> to clear the hotkey.
3. Click on Step 1 under Interact with Target Melee and then select the Action that reads "G -> all". Change the Target of that action to "Group (all of): Melee".
4. Select the DPS 1 Mapped Key in FTL DPS Keys Key Map and select the "Do Interact with Target..." Action. Change the Mapped Key to "Interact with Target Melee".
5. Add only those Characters you want to IWT when you press 1 to the Melee ATG.
6. File, Export and test.
Now, when you press 1, only melee characters will Interact with Target. And you can still use Alt+G to interact with quest givers, loot corpses etc.
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